Perhaps you were using the multimod, and what version of the mod and what version of the game? Because previous runs with the mod were skipping first half of the Realm 3, I think it is fixed now I did a test speedrun with it (version 1.02 of the mod) and saw all scenes.
Or you only lacking those 2 scenes with Kali and nothing else until the Seraphina scene because there is also 4 scenes with Leylala solo, 1 with Naya solo, 1 with Morwen, 1 with Idril and 1 with Kagome if siding with Demons, until the place skip bugged it before. Probably also a few cinematics.
Edit : Also if you gonna use the mod make sure you download the latest version, the one in attachement is still v1.00, use the Mega link to get the v1.02.